AMBER Archive (2006)

Subject: Re: AMBER: "The system has extended beyond" error message

From: David A. Case (case_at_scripps.edu)
Date: Thu May 18 2006 - 07:38:58 CDT

On Thu, May 18, 2006, Atsutoshi Okabe wrote:
>
> I want to simulate in no periodic boundary conditions with explicit water.

Generally, this means you must apply a "cap" of waters, and a constraining
potential to keep the waters from flying off to infinite distance. See
the "fcap" and related variables.

But be aware that a non-periodic simulation with explicit water always has
some problems with the water-vacuum interface, which can significantly affect
the dynamics of the system in a non-physical way. If you do decide this is
what you really need, take a look at igb=10, which uses a dielectric continuum
for regions outside the part of the system that is explicitly represented.
But you might also want to re-think why you are avoiding a periodic system.

...good luck...dac

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